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Title: Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties

Abstract

A fully atomistic modelling of many biophysical and biochemical processes at biologically relevant length- and time scales is beyond our reach with current computational resources, and one approach to overcome this difficulty is the use of multiscale simulation techniques. In such simulations, when system properties necessitate a boundary between resolutions that falls within the solvent region, one can use an approach such as the Adaptive Resolution Scheme (AdResS), in which solvent particles change their resolution on the fly during the simulation. Here, we apply the existing AdResS methodology to biomolecular systems, simulating a fully atomistic protein with an atomistic hydration shell, solvated in a coarse-grained particle reservoir and heat bath. Using as a test case an aqueous solution of the regulatory protein ubiquitin, we first confirm the validity of the AdResS approach for such systems, via an examination of protein and solvent structural and dynamical properties. We then demonstrate how, in addition to providing a computational speedup, such a multiscale AdResS approach can yield otherwise inaccessible physical insights into biomolecular function. We use our methodology to show that protein structure and dynamics can still be correctly modelled using only a few shells of atomistic water molecules. We also discuss aspectsmore » of the AdResS methodology peculiar to biomolecular simulations.« less

Authors:
; ;  [1]
  1. Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany)
Publication Date:
OSTI Identifier:
22415814
Resource Type:
Journal Article
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 142; Journal Issue: 19; Other Information: (c) 2015 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA); Journal ID: ISSN 0021-9606
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; AQUEOUS SOLUTIONS; BIOCHEMISTRY; BIOPHYSICS; HEAT; HYDRATION; MOLECULES; PARTICLES; PROTEIN STRUCTURE; PROTEINS; RESOLUTION; SOLVENTS; WATER

Citation Formats

Fogarty, Aoife C., E-mail: fogarty@mpip-mainz.mpg.de, Potestio, Raffaello, E-mail: potestio@mpip-mainz.mpg.de, and Kremer, Kurt, E-mail: kremer@mpip-mainz.mpg.de. Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties. United States: N. p., 2015. Web. doi:10.1063/1.4921347.
Fogarty, Aoife C., E-mail: fogarty@mpip-mainz.mpg.de, Potestio, Raffaello, E-mail: potestio@mpip-mainz.mpg.de, & Kremer, Kurt, E-mail: kremer@mpip-mainz.mpg.de. Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties. United States. doi:10.1063/1.4921347.
Fogarty, Aoife C., E-mail: fogarty@mpip-mainz.mpg.de, Potestio, Raffaello, E-mail: potestio@mpip-mainz.mpg.de, and Kremer, Kurt, E-mail: kremer@mpip-mainz.mpg.de. Thu . "Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties". United States. doi:10.1063/1.4921347.
@article{osti_22415814,
title = {Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties},
author = {Fogarty, Aoife C., E-mail: fogarty@mpip-mainz.mpg.de and Potestio, Raffaello, E-mail: potestio@mpip-mainz.mpg.de and Kremer, Kurt, E-mail: kremer@mpip-mainz.mpg.de},
abstractNote = {A fully atomistic modelling of many biophysical and biochemical processes at biologically relevant length- and time scales is beyond our reach with current computational resources, and one approach to overcome this difficulty is the use of multiscale simulation techniques. In such simulations, when system properties necessitate a boundary between resolutions that falls within the solvent region, one can use an approach such as the Adaptive Resolution Scheme (AdResS), in which solvent particles change their resolution on the fly during the simulation. Here, we apply the existing AdResS methodology to biomolecular systems, simulating a fully atomistic protein with an atomistic hydration shell, solvated in a coarse-grained particle reservoir and heat bath. Using as a test case an aqueous solution of the regulatory protein ubiquitin, we first confirm the validity of the AdResS approach for such systems, via an examination of protein and solvent structural and dynamical properties. We then demonstrate how, in addition to providing a computational speedup, such a multiscale AdResS approach can yield otherwise inaccessible physical insights into biomolecular function. We use our methodology to show that protein structure and dynamics can still be correctly modelled using only a few shells of atomistic water molecules. We also discuss aspects of the AdResS methodology peculiar to biomolecular simulations.},
doi = {10.1063/1.4921347},
journal = {Journal of Chemical Physics},
issn = {0021-9606},
number = 19,
volume = 142,
place = {United States},
year = {2015},
month = {5}
}